Are you sure that isn't due to duplicates in Apple Mail? If I'm remembering right, things with labels (including "Inbox") will have copies in All Mail as well as each of their label "folders."
IMAP and POP use hierarchical folders and don't understand that a tax email might be marked as both "Government" and "Finances", or whatever your filing system happens to be.
I'm sure that could be an issue as well, but it's not causing the problem in my case.
I've found 1-2 emails in mail from a particular sender, where gmail was unable to find any results, even with their exact address.
I've likewise found perhaps 7/10 of a set of emails in gmail, and found the remaining 3 in mail (while confirming they had unique information not listed in gmail).
IMAP and POP use hierarchical folders and don't understand that a tax email might be marked as both "Government" and "Finances", or whatever your filing system happens to be.